[2017-08-30 13:54:50] Beginning TopHat run (v2.1.1)
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[2017-08-30 13:54:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 13:54:50] Checking for Bowtie index files (genome)..
[2017-08-30 13:54:50] Checking for reference FASTA file
[2017-08-30 13:54:50] Generating SAM header for Bowtie2Index/genome
[2017-08-30 13:54:52] Reading known junctions from GTF file
[2017-08-30 13:54:55] Preparing reads
	 left reads: min. length=50, max. length=50, 26213002 kept reads (2438 discarded)
	right reads: min. length=50, max. length=50, 26126032 kept reads (89408 discarded)
[2017-08-30 14:04:21] Building transcriptome data files /scratch/469154.1.c/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 14:04:31] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 14:10:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:14:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:19:22] Resuming TopHat pipeline with unmapped reads
[2017-08-30 14:19:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:27:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:28:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:28:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:36:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:37:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:38:19] Searching for junctions via segment mapping
[2017-08-30 14:40:29] Retrieving sequences for splices
[2017-08-30 14:41:40] Indexing splices
Building a SMALL index
[2017-08-30 14:41:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:42:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:42:08] Joining segment hits
[2017-08-30 14:43:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:43:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:43:55] Joining segment hits
[2017-08-30 14:45:25] Reporting output tracks
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[2017-08-30 15:14:19] A summary of the alignment counts can be found in /scratch/469154.1.c/tophat2/align_summary.txt
[2017-08-30 15:14:19] Run complete: 01:19:28 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 19 files...